Data and associated files

These are the datasets from the Optimization Strategy 5 (formerly ScatOpt4) and the final genotyping sequencing runs for 200 loci included in the final panel. These microhaplotype genotypes were produced using the Delomas et al., 2023 pipeline as outlined in the article prior to any filtering. microhap_genotypes_final_scat.zip: .csv with microhaplotype genotypes produced from 17 plates of fecal samples in duplicate microhap_genotypes_scatopt4.zip: .csv with microhaplotype genotypes produced from Optimization Strategy 5 (formerly ScatOpt4 in-house) of fecal samples in duplicate. neutral_diagnostic_loci_new.csv: file with diagnostic loci to distinguish between wolves, coyotes, and dogs with original panel amplicon ID as well as chromosome (Chr) and bp positon according to both CamFam6 (Chr, BP) and CanFam3.1(CanFam3.1_Chr, CanFam3.1_BP) populations.haps.vcf: vcf from preliminary genotyping from the Optimization Strategy 2, Test2 (i004) with no ExoSAP treatment and normalization using Just-A-Plate according ot manufacturer instructions; see Methods S.3 for genotyping protocol used; this input was used in the simulation described in Methods S.4 70loci_freq_ScatTest2.csv: empirical frequencies from Optimization Strategy 2, Test2 (i004) with no ExoSAP treatment and normalization using Just-A-Plate according to manufacturer instructions for the 70 loci selected in Optimization Strategy 4; used in simulation to verify there would be sufficiently low PID and PIDsibs gen_data_fecal_2026-06-24.csv: filtered genotype data for neutral loci used in R code final_qpcr_bin_summary.R qPCR_results.csv: qPCR ng/ul results used in R code final_qpcr_bin_summary.R tissue-scat-samples_for-validation-and-error-calculations.csv: empirical data set for determining matching cut-off values OptStrat2-5 (e.g., OptStrat5_200loci_genos_final_sry.zip) zipped folders and Final Scat zipped folder (FinalScat_genos_final_sry.zip) contain zipped summary files and microhaplotype genotypes from each run. barcodes_fieldID.csv: file with sample year numbers to calculate how many samples with SNP genotypes also have microsatellite genotypes pres_abs_genotypes.txt: SRY genotypes from Optimization Strategy 5 used to empirically determine thresholds ScatOpt4KnownSex.csv: samples from Optimization Strategy 5 with known microsatellite sexes used to determine thresholds Clu200_pos_4.txt: file containing the names of the 200 amplicons used in Optimization Strategy 5 and the Final Protocol that correspond to Delomas et al. 2023 naming conventions (primer sequences with adapters can be found in Delomas et al. 2023) Clu334_pos_4.txt: file containing the names of the 334 amplicons used in Optimization Strategies 2 & 3 that correspond to Delomas et al. 2023 naming conventions (primer sequences with adapters can be found in Delomas et al. 2023) Clu70_pos_4.txt: file containing the names of the 70 amplicons used in Optimization Strategies 4 that correspond to Delomas et al. 2023 naming conventions (primer sequences with adapters can be found in Delomas et al. 2023)